6umg

Crystal structure of erenumab Fab bound to the extracellular domain of CGRP receptor

Method: X-RAY DIFFRACTION Dmax: 130.2 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Calcitonin gene-related peptide type 1 receptor

Homo sapiens

UniProt Q16602

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 23–133 Fragment:extracellular domain (UNP residues 23-133) erenumab Fab heavy chain, IgG1 × 1 erenumab Fab light chain, IgG1 × 1 Receptor activity-modifying protein 1 × 1 (O60894) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;0.12 M ethylene glycols, 0.1 M HEPES:MOPS, pH 7.5, 37.5% MPD + PEG1000 + PEG3350 Resolution 2.70 Å R-free 0.282
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain c; UniProt 23–133 Fragment:extracellular domain (UNP residues 23-133) erenumab Fab heavy chain, IgG1 × 1 erenumab Fab light chain, IgG1 × 1 Receptor activity-modifying protein 1 × 1 (O60894) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;0.12 M ethylene glycols, 0.1 M HEPES:MOPS, pH 7.5, 37.5% MPD + PEG1000 + PEG3350 Resolution 2.70 Å R-free 0.282

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

24 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALRL_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 29–139; UniProt 23–133 Author chain c; PDBConstruct 29–139; UniProt 23–133

Receptor activity-modifying protein 1

Homo sapiens

UniProt O60894

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain R; UniProt 26–117 Fragment:extracellular domain (UNP residues 26-117) erenumab Fab heavy chain, IgG1 × 1 erenumab Fab light chain, IgG1 × 1 Calcitonin gene-related peptide type 1 receptor × 1 (Q16602) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;0.12 M ethylene glycols, 0.1 M HEPES:MOPS, pH 7.5, 37.5% MPD + PEG1000 + PEG3350 Resolution 2.70 Å R-free 0.282
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain r; UniProt 26–117 Fragment:extracellular domain (UNP residues 26-117) erenumab Fab heavy chain, IgG1 × 1 erenumab Fab light chain, IgG1 × 1 Calcitonin gene-related peptide type 1 receptor × 1 (Q16602) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;0.12 M ethylene glycols, 0.1 M HEPES:MOPS, pH 7.5, 37.5% MPD + PEG1000 + PEG3350 Resolution 2.70 Å R-free 0.282

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

25 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAMP1_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain R; PDBConstruct 29–120; UniProt 26–117 Author chain r; PDBConstruct 29–120; UniProt 26–117

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6umg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6umg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6umg
Deposition date deposition_date2019-10-09
Structure title titleCrystal structure of erenumab Fab bound to the extracellular domain of CGRP receptor
Keywords keywordsClass B GPCR, Complex, Fragment antigen binding, MEMBRANE PROTEIN-IMMUNE SYSTEM complex; MEMBRANE PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.42
Radius of gyration Rg (electron density) rg_electron37.87
Forward intensity I(0) i0303978000.00
Molecular weight molecular_weight138140.0 kDa
Excluded volume excluded_volume171270 ų
Envelope volume envelope_volume232280 ų
Hydration-shell volume shell_volume51273 ų
Envelope diameter envelope_diameter138.8
Shell Rg shell_rg43.67
Envelope Rg envelope_rg37.38
Shape Rg shape_rg37.83
Total Rg total_rg38.34
Total atoms total_atoms9718
Residues n_residues1259
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax130.2
Rg (real space) rg_real38.41
Rg uncertainty (real space) rg_real_error1.24
I(0) (real space) i0_real3.0400e+08
I(0) uncertainty (real space) i0_real_error5.9640e+06
Rg (reciprocal space) rg_reciprocal38.42
I(0) (reciprocal space) i0_reciprocal304000000.0000
Solution quality estimate total_estimate0.8868
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.5
Skewness Skewness skewness0.310
Kurtosis Kurtosis kurtosis-0.352
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32400000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.911

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd6umgh_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd6umgl1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6umgl2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (8 domains)

Domain ID domain_id6umgH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6umgH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6umgL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6umgL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6umgh01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6umgh02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6umgl01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6umgl02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)